5VRW

Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in non-planar conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RPX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29350 mM imidizole pH 7-7.5, 350 mM sodium acetate, 16-18 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2344.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.7α = 90
b = 79.5β = 107.1
c = 55.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5852.85980.0660.0910.99411.461.97525529-342.01
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.582.61000.4060.5570.6662.021.965

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4RPX2.5852.851258666399.50.23770.23420.306RANDOM35.854
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.030.1-0.130.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_3_deg11.604
r_dihedral_angle_4_deg10.949
r_dihedral_angle_1_deg4.406
r_angle_refined_deg0.893
r_angle_other_deg0.783
r_chiral_restr0.047
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_3_deg11.604
r_dihedral_angle_4_deg10.949
r_dihedral_angle_1_deg4.406
r_angle_refined_deg0.893
r_angle_other_deg0.783
r_chiral_restr0.047
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2573
Nucleic Acid Atoms632
Solvent Atoms48
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
SCALEPACKdata scaling